diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 17b4fa1a7a7..1a1729355d3 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -55,6 +55,9 @@ def main():
     start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ   
     tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' )
     tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' )
+    tool_data_table_config_path = 'tool_data_table_conf.xml'
+    if os.path.exists( 'tool_data_table_conf.test.xml' ):
+        tool_data_table_config_path = 'tool_data_table_conf.test.xml'
     if start_server:
         psu_production = False
         galaxy_test_proxy_port = None
@@ -148,6 +151,7 @@ def main():
                                    datatype_converters_config_file = "datatype_converters_conf.xml.sample",
                                    tool_parse_help = False,
                                    test_conf = "test.conf",
+                                   tool_data_table_config_path = tool_data_table_config_path,
                                    log_destination = "stdout",
                                    use_heartbeat = False,
                                    allow_user_creation = True,
diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml
index 178498dd06e..ad5beb982d5 100644
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -327,8 +327,7 @@
       chrM_base needs to be the base location/name of the index files.
       -->
       <param name="genomeSource" value="indexed" />
-      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
-      <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/chrM" />
+      <param name="index" value="equCab2chrM" />
       <param name="sPaired" value="single" />
       <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
       <param name="sSettingsType" value="preSet" />
@@ -385,8 +384,7 @@
       chrM_base is the index files' location/base name. 
       -->
       <param name="genomeSource" value="indexed" />
-      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
-      <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/chrM" />
+      <param name="index" value="equCab2chrM" />
       <param name="sPaired" value="single" />
       <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
       <param name="sSettingsType" value="full" />